I used to be of the opinion that Resident Evil 4 was a better game, but as the years have gone by I've come to see Vanquish as clearly superior. The only thing RE4 really has over Vanquish (aside from its phenomenal presentation) is that it's a much simpler game and therefore has an easier time forcing the player to come to grips with all its weapons and enemies, even on the relatively easy normal mode. Vanquish, being a much faster-paced game with more wildly different weapons, significantly more movement options, and more complex enemies can't really test the player in the same rigid ways RE4 can - so as a result Vanquish does end up being a bit of a "combat sandbox" game, where it is unfortunately feasible to play through it in ways that aren't very interesting (because the sheer complexity of the game means there's no way for the developers to force you to play in a fun / risky way, similar to the issues I've seen people have with Bayonetta or the Itagaki Ninja Gaiden games - or, to make a more direct comparison, RE6, although that game certainly has other problems).
If you play through it once or twice on the lower difficulty modes I can definitely see Vanquish being a bit underwhelming due to its short length, but as someone who likes replaying games and trying to explore their depth, I agree that Vanquish is probably the best third-person shooter.
Binary Domain isn't really in the conversation at all, I think. It's absolutely a great game but it is tremendously simpler than Vanquish or even Resident Evil 4 (I'll also say here that I don't think RE4 is much weaker than Vanquish, in case this post sounds like I'm ragging on it). BD is really just a rock-solid game that is elevated by its extraordinary presentation, but I don't feel it's comparable to Vanquish in terms of quality.